Grassland ecosystems can provide a variety of services for humans, such as carbon storage, food production, crop pollination and pest regulation. However, grasslands are today one of the most endangered ecosystems due to land use change, agricultural intensification, land abandonment as well as climate change. The present study explores the performance of a knowledge-driven GEOgraphic-Object—based Image Analysis (GEOBIA) learning scheme to classify Very High Resolution (VHR) images for natural grassland ecosystem mapping. The classification was applied to a Natura 2000 protected area in Southern Italy. The Food and Agricultural Organization Land Cover Classification System (FAO-LCCS) hierarchical scheme was instantiated in the learning phase of the algorithm. Four multi-temporal WorldView-2 (WV-2) images were classified by combining plant phenology and agricultural practices rules with prior-image spectral knowledge. Drawing on this knowledge, spectral bands and entropy features from one single date (Post Peak of Biomass) were firstly used for multiple-scale image segmentation into Small Objects (SO) and Large Objects (LO). Thereafter, SO were labelled by considering spectral and context-sensitive features from the whole multi-seasonal data set available together with ancillary data. Lastly, the labelled SO were overlaid to LO segments and, in turn, the latter were labelled by adopting FAO-LCCS criteria about the SOs presence dominance in each LO. Ground reference samples were used only for validating the SO and LO output maps. The knowledge driven GEOBIA classifier for SO classification obtained an OA value of 97.35% with an error of 0.04. For LO classification the value was 75.09% with an error of 0.70. At SO scale, grasslands ecosystem was classified with 92.6%, 99.9% and 96.1% of User’s, Producer’s Accuracy and F1-score, respectively. The findings reported indicate that the knowledge-driven approach not only can be applied for (semi)natural grasslands ecosystem mapping in vast and not accessible areas but can also reduce the costs of ground truth data acquisition. The approach used may provide different level of details (small and large objects in the scene) but also indicates how to design and validate local conservation policies.